R Notebook

Introduction

The purpose of this notebook is to give data locations, data ingestion code, and code for rudimentary analysis and visualization of COVID-19 data provided by New York Times, [NYT1].

The following steps are taken:

• Ingest data

  • Take COVID-19 data from The New York Times, based on reports from state and local health agencies, [NYT1].

  • Take USA counties records data (FIPS codes, geo-coordinates, populations), [WRI1].

• Merge the data.

• Make data summaries and related plots.

• Make corresponding geo-plots.

Note that other, older repositories with COVID-19 data exist, like, [JH1, VK1].

Remark: The time series section is done for illustration purposes only. The forecasts there should not be taken seriously.

Preliminary defintions

From the help of tolower:

capwords <- function(s, strict = FALSE) {
    cap <- function(s) paste(toupper(substring(s, 1, 1)),
                  {s <- substring(s, 2); if(strict) tolower(s) else s},
                             sep = "", collapse = " " )
    sapply(strsplit(s,  split = " "), cap, USE.NAMES = !is.null(names(s)))
}

Import data

NYTimes USA states data

if( !exists("dfNYDataStates") ) {
  dfNYDataStates <- read.csv( "https://raw.githubusercontent.com/nytimes/covid-19-data/master/us-states.csv", stringsAsFactors = FALSE )
  colnames(dfNYDataStates) <- capwords(colnames(dfNYDataStates))
}
head(dfNYDataStates)

dfNYDataStates$DateObject <- as.POSIXct(dfNYDataStates$Date)

summary(as.data.frame(unclass(dfNYDataStates)))

         Date                State           Fips           Cases            Deaths          DateObject                 
 2020-04-09:  56   Washington   :  83   Min.   : 1.00   Min.   :     0   Min.   :   0.00   Min.   :2020-01-21 00:00:00  
 2020-04-10:  56   Illinois     :  80   1st Qu.:17.00   1st Qu.:    11   1st Qu.:   0.00   1st Qu.:2020-03-12 00:00:00  
 2020-04-11:  56   California   :  79   Median :31.00   Median :   144   Median :   2.00   Median :2020-03-23 00:00:00  
 2020-04-12:  56   Arizona      :  78   Mean   :31.11   Mean   :  2515   Mean   :  75.63   Mean   :2020-03-20 12:22:07  
 2020-03-28:  55   Massachusetts:  72   3rd Qu.:46.00   3rd Qu.:  1066   3rd Qu.:  21.00   3rd Qu.:2020-04-02 00:00:00  
 2020-03-29:  55   Wisconsin    :  68   Max.   :78.00   Max.   :188694   Max.   :9385.00   Max.   :2020-04-12 00:00:00  
 (Other)   :1939   (Other)      :1813                                                                                   

NYTimes USA counties data

if(!exists("dfNYDataCounties") ) {
  dfNYDataCounties <- read.csv( "https://raw.githubusercontent.com/nytimes/covid-19-data/master/us-counties.csv", stringsAsFactors = FALSE )
  colnames(dfNYDataCounties) <- capwords(colnames(dfNYDataCounties))
}
head(dfNYDataCounties)

dfNYDataCounties$DateObject <- as.POSIXct(dfNYDataCounties$Date)

summary(as.data.frame(unclass(dfNYDataCounties)))

         Date              County                 State            Fips           Cases              Deaths           DateObject                 
 2020-04-12: 2679   Washington:  682   Georgia       : 3182   Min.   : 1001   Min.   :     0.0   Min.   :   0.000   Min.   :2020-01-21 00:00:00  
 2020-04-11: 2660   Unknown   :  649   Texas         : 3134   1st Qu.:17161   1st Qu.:     2.0   1st Qu.:   0.000   1st Qu.:2020-03-26 00:00:00  
 2020-04-10: 2629   Jefferson :  519   Virginia      : 2205   Median :28135   Median :     5.0   Median :   0.000   Median :2020-04-02 00:00:00  
 2020-04-09: 2595   Franklin  :  478   Indiana       : 1868   Mean   :29529   Mean   :   106.2   Mean   :   3.179   Mean   :2020-03-31 07:50:28  
 2020-04-08: 2565   Jackson   :  423   North Carolina: 1855   3rd Qu.:42125   3rd Qu.:    22.0   3rd Qu.:   1.000   3rd Qu.:2020-04-07 00:00:00  
 2020-04-07: 2539   Montgomery:  398   Tennessee     : 1813   Max.   :56043   Max.   :103208.0   Max.   :6717.000   Max.   :2020-04-12 00:00:00  
 (Other)   :38181   (Other)   :50699   (Other)       :39791   NA's   :716                                                                        

US county records

if(!exists("dfUSACountyData")){
  dfUSACountyData <- read.csv( "https://raw.githubusercontent.com/antononcube/SystemModeling/master/Data/dfUSACountyRecords.csv", stringsAsFactors = FALSE )
}
head(dfUSACountyData)

summary(as.data.frame(unclass(dfUSACountyData)))

         Country          State                   County          FIPS         Population            Lat             Lon         
 UnitedStates:3143   Texas   : 254   WashingtonCounty:  30   Min.   : 1001   Min.   :      89   Min.   :19.60   Min.   :-166.90  
                     Georgia : 159   JeffersonCounty :  25   1st Qu.:18178   1st Qu.:   10980   1st Qu.:34.70   1st Qu.: -98.23  
                     Virginia: 134   FranklinCounty  :  24   Median :29177   Median :   25690   Median :38.37   Median : -90.40  
                     Kentucky: 120   JacksonCounty   :  23   Mean   :30390   Mean   :  102248   Mean   :38.46   Mean   : -92.28  
                     Missouri: 115   LincolnCounty   :  23   3rd Qu.:45082   3rd Qu.:   67507   3rd Qu.:41.81   3rd Qu.: -83.43  
                     Kansas  : 105   MadisonCounty   :  19   Max.   :56045   Max.   :10170292   Max.   :69.30   Max.   : -67.63  
                     (Other) :2256   (Other)         :2999                                                                       

Merge data

dsNYDataCountiesExtended <- 
  dfNYDataCounties %>% 
  dplyr::inner_join( dfUSACountyData %>% dplyr::select_at( .vars = c("FIPS", "Lat", "Lon", "Population") ), by = c( "Fips" = "FIPS" ) )
dsNYDataCountiesExtended

Basic data analysis

ParetoPlotForColumns( dsNYDataCountiesExtended, c("Cases", "Deaths"), scales = "free" )

Geo-histogram

Leaflet

cf <- colorBin( palette = "Reds", domain = log10(dsNYDataCountiesExtended$Cases), bins = 10 )

m <- 
  leaflet( dsNYDataCountiesExtended[, c("Lat", "Lon", "Cases")] ) %>%
  addTiles() %>% 
  addCircleMarkers( ~Lon, ~Lat, radius = ~ log10(Cases), fillColor = ~ cf(log10(Cases)), color = ~ cf(log10(Cases)), fillOpacity = 0.8, stroke = FALSE, popup = ~Cases )
m

Heat-map plots

An alternative of the geo-visualization is to use a heat-map plot.

Cases

Make a heat-map plot by sorting the rows of the cross-tabulation matrix (that correspond to states):

matSDC <- xtabs( Cases ~ State + Date, dfNYDataStates, sparse = TRUE)
d3heatmap::d3heatmap( log10(matSDC+1), cellnote = as.matrix(matSDC), scale = "none", dendrogram = "row", colors = "Blues") #, theme = "dark")

Deaths

Cross-tabulate states with dates over deaths and plot:

matSDD <- xtabs( Deaths ~ State + Date, dfNYDataStates, sparse = TRUE)
d3heatmap::d3heatmap( log10(matSDD+1), cellnote = as.matrix(matSDD), scale = "none", dendrogram = "row", colors = "Blues") #, theme = "dark")

Time series

dfQuery <- 
  dfNYDataStates %>% 
  dplyr::group_by( Date, DateObject ) %>% 
  dplyr::summarise_at( .vars = c("Cases", "Deaths"), .funs = sum )
dfQueryLongForm <- tidyr::pivot_longer( dfQuery, cols = c("Cases", "Deaths"), names_to = "Variable", values_to = "Value")
dfQueryLongForm

ggplot(dfQueryLongForm) +
  geom_line( aes( x = DateObject, y = log10(Value) ) ) +
  facet_wrap( ~Variable, ncol = 1 )

Cases

fit <- forecast::auto.arima( dfQuery$Cases )
fit

Series: dfQuery$Cases 
ARIMA(0,2,0) 

sigma^2 estimated as 3119674:  log likelihood=-720.54
AIC=1443.08   AICc=1443.13   BIC=1445.47

plot( forecast::forecast(fit, h = 20) )
grid(nx = NULL, ny = NULL, col = "lightgray", lty = "dotted")

Deaths

fit <- forecast::auto.arima( dfQuery$Deaths )
fit

Series: dfQuery$Deaths 
ARIMA(1,2,0) 

Coefficients:
          ar1
      -0.3135
s.e.   0.1100

sigma^2 estimated as 18846:  log likelihood=-513.17
AIC=1030.33   AICc=1030.49   BIC=1035.12

plot( forecast::forecast(fit, h = 20) )
grid(nx = NULL, ny = NULL, col = "lightgray", lty = "dotted")